[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?
jalemkul at vt.edu
Sat May 19 17:41:36 CEST 2018
On 5/19/18 8:45 AM, Soham Sarkar wrote:
> Thanks for reply.. but what is the actual pressure of the system? You
> mentioned it as the instantaneous pressure
Instantaneous simply refers to the value at any given time point; these
will fluctuate wildly, particularly for a tiny system like yours, and
the instantaneous values are meaningless.
The average pressure (and its distribution) is more meaningful. Compute
that with gmx energy.
> On Sat, 19 May 2018, 6:03 pm Mark Abraham, <mark.j.abraham at gmail.com> wrote:
>> This is normal for instantaneous measurements of pressure. See
>> On Sat, May 19, 2018, 13:04 Soham Sarkar <soham9038 at gmail.com> wrote:
>>> Dear All,
>>> I have a small system including a 4 residue peptide. I have chosen 8
>>> temperature windows for doing REMD simulation of this system. After the
>>> temperature convergence of the 8 systems in the 1st stage of
>>> run, the obtained pressure are quite absurd, which is not change that
>>> after the 2nd stage of production run. I want to know whether this type
>>> pressure range is ok for a system or not? Should I carry out analysis in
>>> this pressure range? As in normal md simulation there is a pressure
>>> convergence step which takes the system to the desired pressure. This
>>> of step is not there in the REMD simulation.
>>> The pressure and temperature of this system after 1st stage of
>>> equillibration of 10ns are as follows
>>> Temperature(K) Pressure(Bar)
>>> 350.112 -28.4761
>>> 369.218 262.054
>>> 389.201 592.84
>>> 410.074 946.021
>>> 429.12 1273.92
>>> 448.873 1628.61
>>> 469.438 2005.04
>>> 490.272 2392.50
>>> SOHAM SARKAR
>>> Junior Research Fellow
>>> Department of Chemistry
>>> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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